Volume 1 · No. 2 · December 2010 V o lu m e 1 · N o ... - IMA Fungus

Modelling fungal colonies and communities: challenges and opportunities
rapidly increasing computing power, and faster algorithms
for reconstruction and data processing make large volume
scanning at high resolutions feasible. The state-of-the-art
equipment at the UGCT (Centre for X-ray Tomography at
Ghent University) is highly flexible, with in-house developed
software for scanner control, sample reconstruction,
analysis, and visualisation. This set-up allows scanning
with a resolution of 0.2 mm for samples of 37 cm in
diameter down to approximately 400 nm for objects about
the size of a splinter. As such, apart from visualisation, 3D
quantitative information can be retrieved from objects with
a broad range of sizes. Sub-micron resolution scanning
should enable the visualisation of fungal hyphae and by
using time-lapse tomography the growth of these tubular
structures could be monitored (van den Bulcke et al. 2009).
The latter procedure however has associated challenges.
First, fungal growth can interfere with scanning during
moderately long scan times. Second, with lab-based X-ray
sources, polychromatic X-rays, scattering, fluorescence and
noise disturb the ideal acquisition (Vidal et al. 2005). Third,
at sub-micron resolution phase contrast emerges especially
at sharp edges, complicating thresholding and segmentation.
Fourth, tube shift during long scans at sub-micron resolution
can reduce image quality. Fifth, hyphal tubes are hollow
thin-walled structures, as such having a very low X-ray
attenuation. A drastic solution to some of the problems is the
use of synchrotron radiation, having a monochromatic X-ray
bundle, allowing faster scanning with less heating of the
samples, but access to such facilities is a major bottleneck.
Especially the available beam time is limited and as such
this is not an option for long-running experiments, of the
order of days to weeks, and for repeated experiments. Many
of the aforementioned problems are handled at the UGCT
facility. Post-processing can contribute to the enhancement
of image quality; the phase contrast phenomenon can
be solved using dedicated filtering (Boone et al. 2009, De
Witte et al. 2009); and tube shift can be counteracted with
correction software. Proper scanning and processing can
result in the visualization of fungal hyphae as illustrated in
Fig. 2, obtained after scanning of a piece of Pinus sylvestris
subjected to white-rot. In order to study pigmented species
with rather large hyphal structures, such as Aureobasidium
pullulans (van den Bulcke et al. 2008), visualization is easier
due to X-ray interference of the pigment. Apart from individual
hypha tracking, processing of X-ray volumes should enable
the quantification of the effects of material degradation on
different spatial scales, which might be an important concept
to implement a degradation monitoring system. With the
existing scanners, frequent scanning and quantification
of degradation or hyphal biomass on a larger spatial scale
will be a very valuable tool for non-destructive time-lapse
analysis. Advanced algorithms implementing X-ray physics
during reconstruction will increase image quality, whereas
more advanced image processing code will improve
quantitative results. The field of X-ray tomography, both hardand
software, is rapidly evolving and therefore is promising
for in situ fungal monitoring and quantification in wood and
perhaps soil systems in the near future, in addition to other
modalities such as confocal laser microscopy (Hickey et al.
2005) and magnetic resonance imaging (Müller et al. 2002).
Next-generation computational
approaches
Our ability to exploit the experimental advantages described
above is currently constrained by the limited scales at which
existing simulation technologies are able to operate. For
example, in spite of data at larger scales, in Falconer et al.
(2010) we use a domain size for the soil/fungal interactions
of approx 1 cm 3 with a voxel resolution of 30 microns; for
predictions to be useful we need to work at, at the very
ARTICLE
Fig. 2. (a) Three dimensional
rendering of hyphal tubes of a white
rot fungus winding around a small
piece of Pinus sylvestris in contact
with malt extract agar (filling some
cell lumina). (b) Cross-sectional and
(c) longitudinal view illustrating the
high anatomical detail. Bar = 200
µm; voxel size 0.79 µm.
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